Class CollectIlluminaBasecallingMetrics


  • @DocumentedFeature
    public class CollectIlluminaBasecallingMetrics
    extends CommandLineProgram
    A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect. Outputs metrics:
    • Mean Clusters Per Tile
    • Standard Deviation of Clusters Per Tile
    • Mean Pf Clusters Per Tile
    • Standard Deviation of Pf Clusters Per Tile
    • Mean Percentage of Pf Clusters Per Tile
    • Standard Deviation of Percentage of Pf Clusters Per Tile
    • Field Detail

      • BASECALLS_DIR

        @Argument(doc="The Illumina basecalls output directory from which data are read",
                  shortName="B")
        public File BASECALLS_DIR
      • BARCODES_DIR

        @Argument(doc="The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ",
                  shortName="BCD",
                  optional=true)
        public File BARCODES_DIR
      • LANE

        @Argument(doc="The lane whose data will be read",
                  shortName="L")
        public Integer LANE
      • INPUT

        @Argument(doc="The file containing barcodes to expect from the run - barcodeData.#",
                  shortName="I",
                  optional=true)
        public File INPUT
      • READ_STRUCTURE

        @Argument(doc="A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the  data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip).  E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein.",
                  shortName="RS")
        public String READ_STRUCTURE
      • OUTPUT

        @Argument(doc="The file to which the collected metrics are written",
                  shortName="O",
                  optional=true)
        public File OUTPUT
    • Constructor Detail

      • CollectIlluminaBasecallingMetrics

        public CollectIlluminaBasecallingMetrics()
    • Method Detail

      • doWork

        protected int doWork()
        Description copied from class: CommandLineProgram
        Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.